Data in Brief
Transcriptome analysis of bone marrow mesenchymal stromal cells from
patients with primary myelo
fibrosis
Christophe Martinaud, Christophe Desterke, Johanna Konopacki, Alessandro M. Vannucchi, Lisa Pieri,
Paola Guglielmelli, Brigitte Dupriez, Jean-Christophe Ianotto, Laetitia Boutin,
Jean-Jacques Lataillade, Marie-Caroline Le Bousse-Kerdilès
⁎
aINSERM Unit 1197 and UMS33, Paul Brousse Hospital, Andre Lwoff Institute, France bMedicine UFR Paris-Sud University, France
c
Department of Hematology, University of Firenze, Firenze, Italy
d
Department of Hematology, CH Lens, France
e
Department of Hematology, CHU Brest, France
f
Transfusion center of French Army Percy Hospital, France
a b s t r a c t
a r t i c l e i n f o
Article history: Received 23 March 2015
Received in revised form 13 April 2015 Accepted 20 April 2015
Available online 29 April 2015 Keywords:
Primary myelofibrosis Mesenchymal stroma cells Bone marrow
Myeloproliferative disorders
Primary myelofibrosis (PMF) is a clonal myeloproliferative neoplasm whose severity and treatment com-plexity are attributed to the presence of bone marrow (BM)fibrosis and alterations of stroma impairing the production of normal blood cells. Despite the recently discovered mutations including the JAK2V617F mutation in about half of patients, the primitive event responsible for the clonal proliferation is still unknown. In the highly inflammatory context of PMF, the presence of fibrosis associated with a neoangiogenesis and an osteosclerosis concomitant to the myeloproliferation and to the increase number of circulating hematopoietic progenitors suggests that the crosstalk between hematopoietic and stromal cells is deregulated in the PMF BM microenvironmental niches. Within these niches, mesenchymal stro-mal cells (BM-MSC) play a hematopoietic supportive role in the production of growth factors and extra-cellular matrix which regulate the proliferation, differentiation, adhesion and migration of hematopoietic stem/progenitor cells. A transcriptome analysis of BM-MSC in PMF patients will help to characterize their molecular alterations and to understand their involvement in the hematopoietic stem/progenitor cell de-regulation that features PMF.
© 2015 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Specifications
Organism/cell line/tissue Primary mesenchymal stromal cells from human bone marrow
Sex Pathology sex independent
Sequencer or array type Agilent single color Oligo Microarray 4∗ 44k Data format Agilent normalized matrix
Experimental factors Bone marrow from primary myelofibrosis patients versus healthy donors (similar age)
Experimental features Adult (60–80 years old) primary BM-MSCs amplified in vitro for 3 to 5 passages— GSE44426
Consent Helsinki consent Sample source location France and Italia
1. Direct link to deposited data
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44426.
1.1. Experimental design, materials and methods
The transcriptome of medullary stromal cells of patients suffering from primary myelofibrosis was studied by Agilent Oligo microarray technology. The primary myelofibrosis is a chronic myeloproliferative syndrome. To invest the role of bone marrow stroma in the pathophys-iology of this disease, we isolated primary cultured of bone marrow stromal cells from these patients. The osteo-medullary biopsies for the diagnosis of the disease were implanted in DMEM medium with 10% fetal calf serum. Stromal cells during their proliferation adhere to plastic and they were trypsinized between each passage (3–5 passages) when cultures came to confluence. These steps were performed to eliminate
Genomics Data 5 (2015) 1–2
⁎ Corresponding author at: INSERM Unit 1197 and UMS33, Paul Brousse Hospital, Andre Lwoff Institute, France.
http://dx.doi.org/10.1016/j.gdata.2015.04.017
2213-5960/© 2015 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Contents lists available atScienceDirect
Genomics Data
the remaining hematopoietic cell fraction in these cultures. A cytometric control was carried out on the cells prior to performing molecular biology experiments. CD105, CD73 and CD90 marker positivity was verified to validate the mesenchymal cell phenotype. The negativity of the CD45 marker was also carried out to prove the absence of residual hematopoietic cells in culture. Each culture of mesenchymal stromal cell is isolated from the bone marrow of an individual. In total, the bone marrow samples were studied individually from 6 healthy do-nors (6 controls: GSM1084994, GSM1084995, GSM1084996, GSM1084997, GSM1084998, GSM1084999) and from 6 patients with primary myelofibrosis (6 PMF: GSM1085000, GSM1085001, GSM1085002, GSM1085003, GSM1085004, GSM1085005). Concerning the enrollment of control samples: subjects are negative for alcohol abuse and HCV, HBV and HIV virus infections. The choice of control subjects was conditioned by access to bone marrow from subjects having a hip prosthesis surgery: indeed the subjects have an average age similar to that of patients with primary myelofibrosis (between 60 and 80 years). Each sample was treated individually for the extraction of nucleic acids and the achievement of microarrays. RNA was isolated using RNA extraction protocols (NucleoSpin RNA II, Macherey-Nagel) on the Miltenyi plateform. RNA samples were quality-checked via the Agilent 2100 Bioanalyzer (Agilent Technolo-gies). Total RNA sample (1μg) was used for linear T7-based amplifica-tion. RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit/Low RNA Input Linear Amp Kit (Agilent Technolo-gies). The hybridization procedure was performed using Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized
overnight (17 h, 65 °C) to Agilent Whole Human Genome Oligo Micro-arrays 4∗ 44k using Agilent's in hybridization chamber. The fluores-cence signals were detected using Agilent's Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) v9.1 was used to read out and process the microarray imagefiles. The software determines feature intensities including background sub-traction. The signal intensities from single experiment raw data lists are normalized by dividing the intensities values by their median. Normal-ized data were accessible on public database: (GEO submission number
GSE44426, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=
GSE44426), online on Jan. 10, 2015)[1,2]. Appendix A Supplementary data
Supplementary data to this article can be found online athttp://dx. doi.org/10.1016/j.gdata.2015.04.017.
References
[1] C. Martinaud, C. Desterke, J. Konopacki, L. Pieri, R. Golub, S. Schmutz, A. Anginot, B. Guerton, N. Rochet, P. Albanese, E. Henault, O. Pierre-Louis, P. Saint-Blancard, T. de Revel, B. Dupriez, J.-C. Ianoto, M.-F. Bourgeade, A. Vanucchi, J.-J. Lataillade, M.-C. Le Bousse-Kerdilès, Intrinsic increased osteogenic potency of mesenchymal stromal cells in primary myelofibrosis. 2015 (submitted for publication).
[2] C. Desterke, C. Martinaud, B. Guerton, L. Pieri, C. Bogani, D. Clay, F. Torossian, J.-J. Lataillade, H.C. Hasselbach, H. Gisslinger, J.-L. Demory, B. Dupriez, C. Boucheix, E. Rubinstein, S. Amsellem, A.M. Vannucchi, M.-C. Le Bousse-Kerdilès, The tetraspanin CD9 participates in dysmegakaryopoiesis and in stroma interactions in primary my-elofibrosis. Haematologica (2015) (in press).